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Bel Hadj Ali I, Chouaieb H, Saadi Ben Aoun Y, Harigua-Souiai E, Souguir H, Yaacoub A, El Dbouni O, Harrat Z, Mukhtar MM, Ben Said M, Haddad N, Fathallah-Mili A, Guizani I. Dipeptidyl peptidase III as a DNA marker to investigate epidemiology and taxonomy of Old World Leishmania species. PLoS Negl Trop Dis 2021; 15:e0009530. [PMID: 34310607 PMCID: PMC8341715 DOI: 10.1371/journal.pntd.0009530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 08/05/2021] [Accepted: 06/01/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Dipeptidyl peptidase III (DPPIII) member of M49 peptidase family is a zinc-dependent metallopeptidase that cleaves dipeptides sequentially from the N-terminus of its substrates. In Leishmania, DPPIII, was reported with other peptidases to play a significant role in parasites' growth and survival. In a previous study, we used a coding sequence annotated as DPPIII to develop and evaluate a PCR assay that is specific to dermotropic Old World (OW) Leishmania species. Thus, our objective was to further assess use of this gene for Leishmania species identification and for phylogeny, and thus for diagnostic and molecular epidemiology studies of Old World Leishmania species. METHODOLOGY Orthologous DDPIII genes were searched in all Leishmania genomes and aligned to design PCR primers and identify relevant restriction enzymes. A PCR assays was developed and seventy-two Leishmania fragment sequences were analyzed using MEGA X genetics software to infer evolution and phylogenetic relationships of studied species and strains. A PCR-RFLP scheme was also designed and tested on 58 OW Leishmania strains belonging to 8 Leishmania species and evaluated on 75 human clinical skin samples. FINDINGS Sequence analysis showed 478 variable sites (302 being parsimony informative). Test of natural selection (dN-dS) (-0.164, SE = 0.013) inferred a negative selection, characteristic of essential genes, corroborating the DPPIII importance for parasite survival. Inter- and intra-specific genetic diversity was used to develop universal amplification of a 662bp fragment. Sequence analyses and phylogenies confirmed occurrence of 6 clusters congruent to L. major, L. tropica, L. aethiopica, L. arabica, L. turanica, L. tarentolae species, and one to the L. infantum and L. donovani species complex. A PCR-RFLP algorithm for Leishmania species identification was designed using double digestions with HaeIII and KpnI and with SacI and PvuII endonucleases. Overall, this PCR-RFLP yielded distinct profiles for each of the species L. major, L. tropica, L. aethiopica, L. arabica and L. turanica and the L. (Sauroleishmania) L. tarentolae. The species L. donovani, and L. infantum shared the same profile except for strains of Indian origin. When tested on clinical samples, the DPPIII PCR showed sensitivities of 82.22% when compared to direct examination and was able to identify 84.78% of the positive samples. CONCLUSION The study demonstrates that DPPIII gene is suitable to detect and identify Leishmania species and to complement other molecular methods for leishmaniases diagnosis and epidemiology. Thus, it can contribute to evidence-based disease control and surveillance.
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Affiliation(s)
- Insaf Bel Hadj Ali
- Laboratory of Molecular Epidemiology and Experimental Pathology, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunisia
| | - Hamed Chouaieb
- Laboratory of Molecular Epidemiology and Experimental Pathology, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunisia
- Service de parasitologie, EPS Farhat Hached, Faculté de Médecine de Sousse, Université de Sousse, Sousse, Tunisia
| | - Yusr Saadi Ben Aoun
- Laboratory of Molecular Epidemiology and Experimental Pathology, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunisia
| | - Emna Harigua-Souiai
- Laboratory of Molecular Epidemiology and Experimental Pathology, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunisia
| | - Hejer Souguir
- Laboratory of Molecular Epidemiology and Experimental Pathology, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunisia
| | - Alia Yaacoub
- Laboratory of Molecular Epidemiology and Experimental Pathology, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunisia
- Service de parasitologie, EPS Farhat Hached, Faculté de Médecine de Sousse, Université de Sousse, Sousse, Tunisia
| | - Oussaïma El Dbouni
- Department of Infectious Diseases, Rafik Hariri Hospital, Beirut, Lebanon
| | - Zoubir Harrat
- Laboratoire d’Eco-épidémiologie Parasitaire et Génétique des Populations, Institut Pasteur d’Algérie, Algiers, Algeria
| | | | - Moncef Ben Said
- Service de parasitologie, EPS Farhat Hached, Faculté de Médecine de Sousse, Université de Sousse, Sousse, Tunisia
| | - Nabil Haddad
- Laboratory of Immunology and Vector-Borne Diseases, Faculty of Public Health Lebanese University, Hadath, Lebanon
| | - Akila Fathallah-Mili
- Laboratory of Molecular Epidemiology and Experimental Pathology, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunisia
- Service de parasitologie, EPS Farhat Hached, Faculté de Médecine de Sousse, Université de Sousse, Sousse, Tunisia
| | - Ikram Guizani
- Laboratory of Molecular Epidemiology and Experimental Pathology, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunisia
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Chanyalew M, Abebe M, Endale B, Girma S, Tasew G, van Zandbergen G, Ritter U, Gadisa E, Aseffa A, Laskay T. Enhanced production of pro-inflammatory cytokines and chemokines in Ethiopian cutaneous leishmaniasis upon exposure to Leishmania aethiopica. Cytokine 2020; 145:155289. [PMID: 32951968 DOI: 10.1016/j.cyto.2020.155289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/02/2020] [Accepted: 09/06/2020] [Indexed: 11/18/2022]
Abstract
The clinical course and outcome of cutaneous leishmaniasis (CL) vary due to the infecting Leishmania species and host genetic makeup that result in different immune responses against the parasites. The host immune response to Leishmania aethiopica (L.aethiopica), the causative agent of CL in Ethiopia, is poorly understood. To contribute to the understanding of the protective immune response in CL due to L.aethiopica, we characterized the cytokine response to L. aethiopica in patients with the localized form of CL (LCL) and age-and sex-matched apparently healthy controls. By applying a whole blood based in vitro culture we found enhanced release of TNF, IL-6, MCP-1 or CCL2, IP-10 or CXCL10, MIP-1β or CCL4 and IL-8 or CXCL8- but not of IL-10CL patients in response to L. aethiopica compared to the controls. No difference was observed between LCL cases and controls in the secretion of these cytokines and chemokines in whole blood cultures treated with the TLR-ligands LPS, MALP-2 or polyI: C. The observed increased secretion of the pro-inflammatory cytokines/chemokines reflects an enhanced response against the parasites by LCL patients as compared to healthy controls rather than a generally enhanced ability of blood leukocytes from LCL patients to respond to microbial constituents. Our findings suggest that the enhanced production of pro-inflammatory cytokines/chemokines is associated with localized cutaneous leishmaniasis caused by L.aethiopica.
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Affiliation(s)
- Menberework Chanyalew
- Research and Innovation Division, Armauer Hansen Research Institute, P.O. Box 1005, Addis Ababa, Ethiopia.
| | - Markos Abebe
- Research and Innovation Division, Armauer Hansen Research Institute, P.O. Box 1005, Addis Ababa, Ethiopia
| | - Birtukan Endale
- Research and Innovation Division, Armauer Hansen Research Institute, P.O. Box 1005, Addis Ababa, Ethiopia
| | - Selfu Girma
- Research and Innovation Division, Armauer Hansen Research Institute, P.O. Box 1005, Addis Ababa, Ethiopia
| | - Geremew Tasew
- Research and Innovation Division, Armauer Hansen Research Institute, P.O. Box 1005, Addis Ababa, Ethiopia; Leishmaniasis Research Laboratory, Ethiopia Public Health Institute, P.O. Box 1242, Addis Ababa, Ethiopia
| | - Ger van Zandbergen
- Division of Immunology, Paul-Ehrlich-Institute, Federal Institute for Vaccines and Biomedicines, Langen D-63225, Germany.
| | - Uwe Ritter
- Regensburg Center for Interventional Immunology (RCI), Institute of Immunology, University Medical Center Regensburg, University of Regensburg, D-93053 Regensburg, Germany.
| | - Endalamaw Gadisa
- Research and Innovation Division, Armauer Hansen Research Institute, P.O. Box 1005, Addis Ababa, Ethiopia
| | - Abraham Aseffa
- Research and Innovation Division, Armauer Hansen Research Institute, P.O. Box 1005, Addis Ababa, Ethiopia
| | - Tamás Laskay
- Department of Infectious Diseases and Microbiology, University of Lübeck, D-23560 Lübeck, Germany.
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van Henten S, Adriaensen W, Fikre H, Akuffo H, Diro E, Hailu A, Van der Auwera G, van Griensven J. Cutaneous Leishmaniasis Due to Leishmania aethiopica. EClinicalMedicine 2018; 6:69-81. [PMID: 31193672 PMCID: PMC6537575 DOI: 10.1016/j.eclinm.2018.12.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 12/21/2018] [Accepted: 12/24/2018] [Indexed: 01/06/2023] Open
Abstract
Leishmania aethiopica is the main causative species for cutaneous leishmaniasis (CL) in Ethiopia. Despite its considerable burden, L. aethiopica has been one of the most neglected Leishmania species. In this review, published evidence on L. aethiopica history, geography, vector, reservoir, epidemiology, parasitology, and immunology is discussed and knowledge gaps are outlined. L. aethiopica endemic regions are limited to the highland areas, although nationwide studies on CL prevalence are lacking. Phlebotomus pedifer and P. longipes are the sandfly vectors and hyraxes are considered to be the main reservoir, but the role of other sandfly species and other potential reservoirs requires further investigation. Where and how transmission occurs exactly are also still unknown. Most CL patients in Ethiopia are children and young adults. Lesions are most commonly on the face, in contrast to CL caused by other Leishmania species which may more frequently affect other body parts. CL lesions caused by L. aethiopica seem atypical and more severe in their presentation as compared to other Leishmania species. Mucocutaneous leishmaniasis and diffuse cutaneous leishmaniasis are relatively common, and healing of lesions caused by L. aethiopica seems to take longer than that of other species. A thorough documentation of the natural evolution of L. aethiopica as well as in depth studies into the immunological and parasitological characteristics that underpin the atypical and severe clinical presentation are needed. Better understanding of CL caused by this parasite species will contribute to interventions related to transmission, prevention, and treatment.
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Affiliation(s)
- Saskia van Henten
- Unit of HIV and Neglected Tropical Diseases, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Wim Adriaensen
- Unit of HIV and Neglected Tropical Diseases, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Helina Fikre
- Leishmania Research and Treatment Center, University of Gondar Hospital, Gondar, Ethiopia
| | - Hannah Akuffo
- Swedish International Development Agency (Sida) and Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Solna, Sweden
| | - Ermias Diro
- Leishmania Research and Treatment Center, University of Gondar Hospital, Gondar, Ethiopia
| | - Asrat Hailu
- Addis Ababa University School of Medicine, Ethiopia
| | - Gert Van der Auwera
- Unit of Molecular Parasitology, Institute of Tropical Medicine, Department of Biomedical Sciences, Antwerp, Belgium
| | - Johan van Griensven
- Unit of HIV and Neglected Tropical Diseases, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
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Curvas de fusión de regiones genómicas específicas: una herramienta prometedora para el diagnóstico y tipificación de las especies causantes de la leishmaniasis cutánea en Colombia. BIOMEDICA 2017. [PMID: 29518886 DOI: 10.7705/biomedica.v37i4.3634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Introducción. La leishmaniasis cutánea es una enfermedad causada por parásitos del género Leishmania que tiene gran incidencia en Colombia. El diagnóstico y la identificación de la especie infecciosa son factores críticos en el momento de escoger e iniciar el tratamiento. Actualmente, los métodos de diagnóstico y tipificación requieren procedimientos complejos, por lo que es necesario validar nuevos marcadores moleculares y métodos que simplifiquen el proceso.Objetivo. Desarrollar una herramienta basada en la reacción en cadena de la polimerasa (PCR) con curvas de fusión (High Resolution Melting; PCR-HRM) para el diagnóstico y tipificación de las tres especies de Leishmania de importancia epidemiológica en casos de leishmaniasis cutánea en Colombia.Materiales y métodos. Los genomas de Leishmania panamensis, L. braziliensis y L. guyanensis se compararon mediante métodos bioinformáticos. Las regiones específicas de especie identificadas se validaron mediante PCR. Para los marcadores seleccionados se diseñó una PCR-HRM y se estimaron algunos parámetros de validez y seguridad usando aislamientos de pacientes colombianos caracterizados previamente mediante PCR y análisis de polimorfismos en la longitud de los fragmentos de restricción (Restriction Fragment Length Polymorphism - RFLP; PCR-RFLP) del gen hsp70.Resultados. El análisis genómico comparativo mostró 24 regiones específicas de especie. Sin embargo, la validación mediante PCR solo identificó un marcador específico para cada especie de Leishmania. Los otros marcadores mostraron amplificación cruzada. El límite de detección para los tres marcadores seleccionados fue de un parásito, mientras que la sensibilidad, la especificidad, el valor predictivo positivo y el negativo fueron de 91,4, 100, 100 y 75 %, respectivamente.Conclusiones. Las tres regiones seleccionadas pueden emplearse como marcadores moleculares en el diagnóstico y tipificación de las especies causantes de la leishmaniasis cutánea en Colombia.
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Coupat-Goutaland B, Régoudis E, Besseyrias M, Mularoni A, Binet M, Herbelin P, Pélandakis M. Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers. PLoS One 2016; 11:e0152434. [PMID: 27035434 PMCID: PMC4818093 DOI: 10.1371/journal.pone.0152434] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 03/14/2016] [Indexed: 11/19/2022] Open
Abstract
Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains.
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Affiliation(s)
- Bénédicte Coupat-Goutaland
- Univ Lyon, Université Lyon 1, CNRS UMR 5240 Microbiology Adaptation and Pathogenesis, Villeurbanne, France
| | - Estelle Régoudis
- Univ Lyon, Université Lyon 1, CNRS UMR 5240 Microbiology Adaptation and Pathogenesis, Villeurbanne, France
| | | | - Angélique Mularoni
- Univ Lyon, Université Lyon 1, ISPB EA 4446 Bioactive Molecules and Medicinal Chemistry, Lyon, France
| | - Marie Binet
- EDF Research and Development, Laboratoire National d’Hydraulique et Environnement, Chatou, France
| | - Pascaline Herbelin
- EDF Research and Development, Laboratoire National d’Hydraulique et Environnement, Chatou, France
| | - Michel Pélandakis
- Univ Lyon, Université Lyon 1, CNRS UMR 5240 Microbiology Adaptation and Pathogenesis, Villeurbanne, France
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Ribolla PEM, Gushi LT, Pires e Cruz MDS, Costa CHN, Costa DL, Lima Júnior MSDC, Dorval MEMC, Gutierrez de Oliveira A, da Cunha Santos MF, Fonseca Camargo-Neves VL, Fortaleza CMCB, Alonso DP. Leishmania infantum Genetic Diversity and Lutzomyia longipalpis Mitochondrial Haplotypes in Brazil. BIOMED RESEARCH INTERNATIONAL 2016; 2016:9249217. [PMID: 27119085 PMCID: PMC4828539 DOI: 10.1155/2016/9249217] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/22/2016] [Accepted: 03/07/2016] [Indexed: 02/07/2023]
Abstract
Leishmania infantum is the etiological agent of visceral leishmaniasis (VL) in the Americas with domestic dogs being its major reservoir hosts. The main VL vector is the sandfly Lutzomyia longipalpis, while other Lutzomyia species may play a role in disease transmission. Although the genetic structure of L. infantum populations has been widely evaluated, only a few studies have addressed this subject coupled to the genetic structure of the respective sandfly vectors. In this study, we analyzed the population structure of L. infantum in three major VL endemic areas in Brazil and associated it with Lutzomyia longipalpis geographic structure.
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Affiliation(s)
- Paulo Eduardo Martins Ribolla
- Departamento de Parasitologia, Universidade Estadual Paulista “Júlio de Mesquita Filho” (UNESP), Instituto de Biotecnologia de Botucatu (IBTEC), 18607-440 Botucatu, SP, Brazil
| | - Letícia Tsieme Gushi
- Departamento de Parasitologia, Universidade Estadual Paulista “Júlio de Mesquita Filho” (UNESP), Instituto de Biotecnologia de Botucatu (IBTEC), 18607-440 Botucatu, SP, Brazil
| | - Maria do Socorro Pires e Cruz
- Departamento de Morfofisiologia Veterinária Centro de Ciências Agrárias, Universidade Federal do Piauí, 64049-550 Teresina, PI, Brazil
| | - Carlos Henrique Nery Costa
- Laboratório de Pesquisa em Leishmaniose Visceral, Instituto de Doenças Tropicais Natan Portella, 64001-450 Teresina, PI, Brazil
| | - Dorcas Lamounier Costa
- Laboratório de Pesquisa em Leishmaniose Visceral, Instituto de Doenças Tropicais Natan Portella, 64001-450 Teresina, PI, Brazil
| | | | | | - Alessandra Gutierrez de Oliveira
- Programa de Pós-Graduação em Doenças Infecciosas e Parasitárias, Faculdade de Medicina (FAMED), Universidade Federal de Mato Grosso do Sul (UFMS), 79070-900 Campo Grande, MS, Brazil
| | - Mirella Ferreira da Cunha Santos
- Programa de Pós-Graduação em Doenças Infecciosas e Parasitárias, Faculdade de Medicina (FAMED), Universidade Federal de Mato Grosso do Sul (UFMS), 79070-900 Campo Grande, MS, Brazil
| | | | - Carlos Magno Castello Branco Fortaleza
- Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, Universidade Estadual Paulista “Júlio de Mesquita Filho” (UNESP), 18618-687 Botucatu, SP, Brazil
| | - Diego Peres Alonso
- Departamento de Parasitologia, Universidade Estadual Paulista “Júlio de Mesquita Filho” (UNESP), Instituto de Biotecnologia de Botucatu (IBTEC), 18607-440 Botucatu, SP, Brazil
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The Genetic Relationship between Leishmania aethiopica and Leishmania tropica Revealed by Comparing Microsatellite Profiles. PLoS One 2015. [PMID: 26196393 PMCID: PMC4511230 DOI: 10.1371/journal.pone.0131227] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Leishmania (Leishmania) aethiopica and L. (L.) tropica cause cutaneous leishmaniases and appear to be related. L. aethiopica is geographically restricted to Ethiopia and Kenya; L. tropica is widely dispersed from the Eastern Mediterranean, through the Middle East into eastern India and in north, east and south Africa. Their phylogenetic inter-relationship is only partially revealed. Some studies indicate a close relationship. Here, eight strains of L. aethiopica were characterized genetically and compared with 156 strains of L. tropica from most of the latter species' geographical range to discern the closeness. METHODOLOGY/PRINCIPAL FINDINGS Twelve unlinked microsatellite markers previously used to genotype strains of L. tropica were successfully applied to the eight strains of L. aethiopica and their microsatellite profiles were compared to those of 156 strains of L. tropica from various geographical locations that were isolated from human cases of cutaneous and visceral leishmaniasis, hyraxes and sand fly vectors. All the microsatellite profiles were subjected to various analytical algorithms: Bayesian statistics, distance-based and factorial correspondence analysis, revealing: (i) the species L. aethiopica, though geographically restricted, is genetically very heterogeneous; (ii) the strains of L. aethiopica formed a distinct genetic cluster; and (iii) strains of L. aethiopica are closely related to strains of L. tropica and more so to the African ones, although, by factorial correspondence analysis, clearly separate from them. CONCLUSIONS/SIGNIFICANCE The successful application of the 12 microsatellite markers, originally considered species-specific for the species L. tropica, to strains of L. aethiopica confirmed the close relationship between these two species. The Bayesian and distance-based methods clustered the strains of L. aethiopica among African strains of L. tropica, while the factorial correspondence analysis indicated a clear separation between the two species. There was no correlation between microsatellite profiles of the eight strains of L. aethiopica and the type of leishmaniasis, localized (LCL) versus diffuse cutaneous leishmaniasis (DCL), displayed by the human cases.
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Aluru S, Hide M, Michel G, Bañuls AL, Marty P, Pomares C. Multilocus microsatellite typing of Leishmania and clinical applications: a review. ACTA ACUST UNITED AC 2015; 22:16. [PMID: 25950900 PMCID: PMC4423940 DOI: 10.1051/parasite/2015016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 04/17/2015] [Indexed: 12/03/2022]
Abstract
Microsatellite markers have been used for Leishmania genetic studies worldwide, giving useful insight into leishmaniasis epidemiology. Understanding the geographic distribution, dynamics of Leishmania populations, and disease epidemiology improved markedly with this tool. In endemic foci, the origins of antimony-resistant strains and multidrug treatment failures were explored with multilocus microsatellite typing (MLMT). High genetic variability was detected but no association between parasite genotypes and drug resistance was established. An association between MLMT profiles and clinical disease manifestations was highlighted in only three studies and this data needs further confirmation. At the individual level, MLMT provided information on relapse and reinfection when multiple leishmaniasis episodes occurred. This information could improve knowledge of epidemiology and guide therapeutic choices for active chronic visceral leishmaniasis, the disease form in some HIV-positive patients.
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Affiliation(s)
- Srikanth Aluru
- Aix-Marseille Université, Marseille, France - INSERM, U1065, Centre Méditerranéen de Médecine Moléculaire, C3M, Toxines Microbiennes dans la Relation Hôte Pathogènes, 06204 Nice Cedex 3, France
| | - Mallorie Hide
- UMR MIVEGEC IRD 224-CNRS 5290, Universités Montpellier 1 et 2, Montpellier, France
| | - Gregory Michel
- INSERM, U1065, Centre Méditerranéen de Médecine Moléculaire, C3M, Toxines Microbiennes dans la Relation Hôte Pathogènes, 06204 Nice Cedex 3, France - Université de Nice Sophia Antipolis, Faculté de Médecine, 06107 Nice Cedex 2, France
| | - Anne-Laure Bañuls
- UMR MIVEGEC IRD 224-CNRS 5290, Universités Montpellier 1 et 2, Montpellier, France
| | - Pierre Marty
- INSERM, U1065, Centre Méditerranéen de Médecine Moléculaire, C3M, Toxines Microbiennes dans la Relation Hôte Pathogènes, 06204 Nice Cedex 3, France - Université de Nice Sophia Antipolis, Faculté de Médecine, 06107 Nice Cedex 2, France - Parasitologie-Mycologie, Centre Hospitalier Universitaire l'Archet, CS 23079, 06202 Nice Cedex 3, France
| | - Christelle Pomares
- INSERM, U1065, Centre Méditerranéen de Médecine Moléculaire, C3M, Toxines Microbiennes dans la Relation Hôte Pathogènes, 06204 Nice Cedex 3, France - Université de Nice Sophia Antipolis, Faculté de Médecine, 06107 Nice Cedex 2, France - Parasitologie-Mycologie, Centre Hospitalier Universitaire l'Archet, CS 23079, 06202 Nice Cedex 3, France
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Králová-Hromadová I, Minárik G, Bazsalovicsová E, Mikulíček P, Oravcová A, Pálková L, Hanzelová V. Development of microsatellite markers in Caryophyllaeus laticeps (Cestoda: Caryophyllidea), monozoic fish tapeworm, using next-generation sequencing approach. Parasitol Res 2014; 114:721-6. [PMID: 25482859 DOI: 10.1007/s00436-014-4239-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/14/2014] [Indexed: 01/30/2023]
Abstract
Caryophyllaeus laticeps (Pallas 1781) (Cestoda: Caryophyllidea) is a monozoic tapeworm of cyprinid fishes with a distribution area that includes Europe, most of the Palaearctic Asia and northern Africa. Broad geographic distribution, wide range of definitive fish hosts and recently revealed high morphological plasticity of the parasite, which is not in an agreement with molecular findings, make this species to be an interesting model for population biology studies. Microsatellites (short tandem repeat (STR) markers), as predominant markers for population genetics, were designed for C. laticeps using a next-generation sequencing (NGS) approach. Out of 165 marker candidates, 61 yielded PCR products of the expected size and in 25 of the candidates a declared repetitive motif was confirmed by Sanger sequencing. After the fragment analysis, six loci were proved to be polymorphic and tested for heterozygosity, Hardy-Weinberg equilibrium and the presence of null alleles on 59 individuals coming from three geographically widely separated populations (Slovakia, Russia and UK). The number of alleles in particular loci and populations ranged from two to five. Significant deficit of heterozygotes and the presence of null alleles were found in one locus in all three populations. Other loci showed deviations from Hardy-Weinberg equilibrium and the presence of null alleles only in some populations. In spite of relatively low polymorphism and the potential presence of null alleles, newly developed microsatellites may be applied as suitable markers in population genetic studies of C. laticeps.
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Dikhit MR, Moharana KC, Sahoo BR, Sahoo GC, Das P. LeishMicrosatDB: open source database of repeat sequences detected in six fully sequenced Leishmania genomes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau078. [PMID: 25125444 PMCID: PMC4132413 DOI: 10.1093/database/bau078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
UNLABELLED A Leishmania Microsatellite Database (LeishMicrosatDB) is reported for genome wise mining of microsatellites in six Leishmania species, using in silico techniques. This was created to provide parasitologists a platform to understand the genome characterization, mapping, phylogeny and evolutionary analysis. The present version of the database contains 1,738,669 simple sequence repeats of which 181 s756 repeats are present in compound form. The repeats can be sought in a chromosome using input parameters such as repeat type (mono- hexa), coding status, repeat unit length and repeat sequence motif. The genic repeats have been further hyperlinked with their corresponding locus id, and the database is appended with primer3 plus for primer designing of selected repeats with left and right flanking sequences up to 250 bp. Information on clustering and polymorphic repeats can also be retrieved. This database may also be adopted as a tool to study the relative occurrence and distribution of microsatellites across the parasitic genome. The database can enable a biologist to select markers at desired intervals over the chromosomes, and can be accessed as an open source repository at http://biomedinformri.com/leishmicrosat. DATABASE URL http://biomedinformri.com/leishmicrosat.
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Affiliation(s)
- Manas R Dikhit
- Biomedical Informatics Center and Department of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - Kanhu C Moharana
- Biomedical Informatics Center and Department of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - Bikash R Sahoo
- Biomedical Informatics Center and Department of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - Ganesh C Sahoo
- Biomedical Informatics Center and Department of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - Pradeep Das
- Biomedical Informatics Center and Department of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, IndiaBiomedical Informatics Center and Department of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
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